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style: format code with isort and Yapf #39

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86 changes: 55 additions & 31 deletions tests/test_hsf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,14 +59,22 @@ def config(models_path):
"execution_providers": [
[
"CUDAExecutionProvider",
{"device_id": 0, "gpu_mem_limit": 2147483648},
{
"device_id": 0,
"gpu_mem_limit": 2147483648
},
],
"CPUExecutionProvider",
],
"batch_size": 1,
"batch_size":
1,
},
},
"roiloc": {"roi": "hippocampus", "contrast": "t2", "margin": [2, 0, 2]},
"roiloc": {
"roi": "hippocampus",
"contrast": "t2",
"margin": [2, 0, 2]
},
"augmentation": {
"flip": {
"axes": ["LR"],
Expand All @@ -89,18 +97,24 @@ def config(models_path):
"multispectrality": {
"pattern": None,
"same_space": True,
"registration": {"type_of_transform": "AffineFast"},
"registration": {
"type_of_transform": "AffineFast"
},
},
"segmentation": {
"ca_mode": "1/2/3",
"models_path": str(models_path),
"models": {
"model.onnx": {
"url": "https://zenodo.org/record/6457484/files/arunet_3.0.0_single.onnx?download=1",
"url":
"https://zenodo.org/record/6457484/files/arunet_3.0.0_single.onnx?download=1",
"xxh3_64": "71edec9011f7f304",
}
},
"segmentation": {"test_time_augmentation": True, "test_time_num_aug": 5},
"segmentation": {
"test_time_augmentation": True,
"test_time_num_aug": 5
},
},
}

Expand All @@ -112,9 +126,9 @@ def deepsparse_inference_engines(models_path):
"""Tests that models can be loaded using DeepSparse"""
settings = DictConfig({"num_cores": 0, "batch_size": 2})

engines = hsf.engines.get_inference_engines(
models_path, engine_name="deepsparse", engine_settings=settings
)
engines = hsf.engines.get_inference_engines(models_path,
engine_name="deepsparse",
engine_settings=settings)

return list(engines)

Expand Down Expand Up @@ -157,13 +171,16 @@ def test_roiloc(models_path):

mri, mask = hsf.roiloc_wrapper.get_mri(mris[0], mask_pattern="mask.nii.gz")
assert isinstance(mask, ants.ANTsImage)
mri, mask = hsf.roiloc_wrapper.get_mri(mris[0], mask_pattern="no_mask.nii.gz")
mri, mask = hsf.roiloc_wrapper.get_mri(mris[0],
mask_pattern="no_mask.nii.gz")
assert isinstance(mri, ants.ANTsImage)
assert mask is None

_, right, left = hsf.roiloc_wrapper.get_hippocampi(
mri, {"contrast": "t2", "margin": [2, 0, 2], "roi": "hippocampus"}, mask
)
_, right, left = hsf.roiloc_wrapper.get_hippocampi(mri, {
"contrast": "t2",
"margin": [2, 0, 2],
"roi": "hippocampus"
}, mask)

assert isinstance(right, ants.ANTsImage)
assert isinstance(left, ants.ANTsImage)
Expand Down Expand Up @@ -195,33 +212,40 @@ def test_segment(models_path, config, deepsparse_inference_engines):

def test_multispectrality(models_path):
"""Tests that we can co-locate hippocampi in another contrast."""
config = DictConfig(
{
"files": {"output_dir": str(models_path)},
"multispectrality": {
"pattern": "sub0_tse.nii.gz",
"same_space": False,
"registration": {"type_of_transform": "AffineFast"},
config = DictConfig({
"files": {
"output_dir": str(models_path)
},
"multispectrality": {
"pattern": "sub0_tse.nii.gz",
"same_space": False,
"registration": {
"type_of_transform": "AffineFast"
},
}
)
},
})

mri = hsf.roiloc_wrapper.load_from_config(models_path, "sub0_tse.nii.gz")[0]
second_contrast = hsf.multispectrality.get_second_contrast(mri, "sub0_tse.nii.gz")
mri = hsf.roiloc_wrapper.load_from_config(models_path,
"sub0_tse.nii.gz")[0]
second_contrast = hsf.multispectrality.get_second_contrast(
mri, "sub0_tse.nii.gz")

registered = hsf.multispectrality.register(
mri, second_contrast, DictConfig({"multispectrality": {"same_space": True}})
)
mri, second_contrast,
DictConfig({"multispectrality": {
"same_space": True
}}))
registered = hsf.multispectrality.register(mri, second_contrast, config)

img = ants.image_read(str(mri), reorient="LPI")
locator, _, _ = hsf.roiloc_wrapper.get_hippocampi(
img, {"contrast": "t2", "margin": [2, 0, 2], "roi": "hippocampus"}, None
)
locator, _, _ = hsf.roiloc_wrapper.get_hippocampi(img, {
"contrast": "t2",
"margin": [2, 0, 2],
"roi": "hippocampus"
}, None)

_, _ = hsf.multispectrality.get_additional_hippocampi(
mri, registered, locator, config
)
mri, registered, locator, config)


def test_uncertainty():
Expand Down